[2024-01-24 12:29:28,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg03e58861-6acb-447e-bc82-911ef6687f39/dqc_reference
[2024-01-24 12:29:29,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:29,788] [INFO] Task started: Prodigal
[2024-01-24 12:29:29,789] [INFO] Running command: gunzip -c /var/lib/cwl/stg28b44ceb-3658-424e-9c1c-a5fecdaef4d6/GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/cds.fna -a GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:44,001] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:44,001] [INFO] Task started: HMMsearch
[2024-01-24 12:29:44,001] [INFO] Running command: hmmsearch --tblout GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03e58861-6acb-447e-bc82-911ef6687f39/dqc_reference/reference_markers.hmm GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:44,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:44,388] [INFO] Found 6/6 markers.
[2024-01-24 12:29:44,431] [INFO] Query marker FASTA was written to GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:29:44,431] [INFO] Task started: Blastn
[2024-01-24 12:29:44,432] [INFO] Running command: blastn -query GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg03e58861-6acb-447e-bc82-911ef6687f39/dqc_reference/reference_markers.fasta -out GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:45,654] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:45,658] [INFO] Selected 14 target genomes.
[2024-01-24 12:29:45,659] [INFO] Target genome list was writen to GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:29:45,677] [INFO] Task started: fastANI
[2024-01-24 12:29:45,677] [INFO] Running command: fastANI --query /var/lib/cwl/stg28b44ceb-3658-424e-9c1c-a5fecdaef4d6/GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna.gz --refList GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:02,332] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:02,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03e58861-6acb-447e-bc82-911ef6687f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:02,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03e58861-6acb-447e-bc82-911ef6687f39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:02,346] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:02,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:02,346] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	100.0	1549	1552	95	conclusive
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	92.8919	1228	1552	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	89.7936	1098	1552	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	89.1191	1132	1552	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	83.561	751	1552	95	below_threshold
Azotobacter chroococcum	strain=ATCC 9043	GCA_004327905.1	353	353	type	True	83.5269	829	1552	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.4501	823	1552	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	83.2011	731	1552	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	82.7491	776	1552	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	82.6934	662	1552	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	82.0837	694	1552	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	81.7529	690	1552	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	80.9524	608	1552	95	below_threshold
Serpens gallinarum	strain=Sa2CUA2	GCA_014836765.1	2763075	2763075	type	True	80.6544	557	1552	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:02,348] [INFO] DFAST Taxonomy check result was written to GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:30:02,349] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:02,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:02,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03e58861-6acb-447e-bc82-911ef6687f39/dqc_reference/checkm_data
[2024-01-24 12:30:02,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:02,406] [INFO] Task started: CheckM
[2024-01-24 12:30:02,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/checkm_input GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:30:47,421] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:47,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:47,442] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:47,442] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:47,443] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:30:47,443] [INFO] Task started: Blastn
[2024-01-24 12:30:47,443] [INFO] Running command: blastn -query GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg03e58861-6acb-447e-bc82-911ef6687f39/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:49,894] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:49,897] [INFO] Selected 8 target genomes.
[2024-01-24 12:30:49,898] [INFO] Target genome list was writen to GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:49,912] [INFO] Task started: fastANI
[2024-01-24 12:30:49,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg28b44ceb-3658-424e-9c1c-a5fecdaef4d6/GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna.gz --refList GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:00,066] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:00,075] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:00,075] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900109175.1	s__Pseudomonas_K linyingensis	100.0	1549	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900115715.1	s__Pseudomonas_K sagittaria	92.9013	1227	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	89.8561	1044	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_019097855.1	s__Pseudomonas_K sp019097855	89.8148	1096	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	89.1289	1131	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105885.1	s__Pseudomonas_K guangdongensis	87.8987	824	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.99	98.99	0.99	0.99	2	-
GCF_009363155.1	s__Azotobacter salinestris	82.9848	816	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Azotobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000412695.1	s__Pseudomonas_F resinovorans_A	82.4113	858	1552	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:00,077] [INFO] GTDB search result was written to GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:00,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:00,084] [INFO] DFAST_QC result json was written to GCF_900109175.1_IMG-taxon_2663762776_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:31:00,084] [INFO] DFAST_QC completed!
[2024-01-24 12:31:00,084] [INFO] Total running time: 0h1m32s